Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <TysonNovak2001OdeSystem.hpp>
Public Member Functions | |
TysonNovak2001OdeSystem (std::vector< double > stateVariables=std::vector< double >()) | |
~TysonNovak2001OdeSystem () | |
void | Init () |
void | EvaluateYDerivatives (double time, const std::vector< double > &rY, std::vector< double > &rDY) |
bool | CalculateStoppingEvent (double time, const std::vector< double > &rY) |
double | CalculateRootFunction (double time, const std::vector< double > &rY) |
virtual void | AnalyticJacobian (const std::vector< double > &rSolutionGuess, double **jacobian, double time, double timeStep) |
Public Member Functions inherited from AbstractOdeSystemWithAnalyticJacobian | |
AbstractOdeSystemWithAnalyticJacobian (unsigned numberOfStateVariables=0) | |
Public Member Functions inherited from AbstractOdeSystem | |
AbstractOdeSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractOdeSystem () |
bool | GetUseAnalyticJacobian () |
const std::vector< double > & | rGetConstStateVariables () const |
Public Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
AbstractParameterisedSystem (unsigned numberOfStateVariables) | |
std::vector< double > & | rGetStateVariables () |
std::vector< double > | GetStateVariables () |
void | SetStateVariables (const std::vector< double > &rStateVariables) |
double | GetStateVariable (unsigned index) const |
double | GetStateVariable (const std::string &rName) const |
void | SetStateVariable (unsigned index, double newValue) |
void | SetStateVariable (const std::string &rName, double newValue) |
virtual void | VerifyStateVariables () |
void | SetDefaultInitialConditions (const std::vector< double > &rInitialConditions) |
void | SetDefaultInitialCondition (unsigned index, double initialCondition) |
std::vector< double > | GetInitialConditions () const |
void | ResetToInitialConditions () |
double | GetParameter (unsigned index) const |
double | GetParameter (const std::string &rName) const |
void | SetParameter (const std::string &rName, double value) |
void | SetParameter (unsigned index, double value) |
double | GetAnyVariable (unsigned index, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
double | GetAnyVariable (const std::string &rName, double time=0.0, std::vector< double > *pDerivedQuantities=NULL) |
void | SetAnyVariable (unsigned index, double value) |
void | SetAnyVariable (const std::string &rName, double value) |
virtual std::vector< double > | ComputeDerivedQuantities (double time, const std::vector< double > &rState) |
std::vector< double > | ComputeDerivedQuantitiesFromCurrentState (double time) |
Public Member Functions inherited from AbstractUntemplatedParameterisedSystem | |
AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables) | |
virtual | ~AbstractUntemplatedParameterisedSystem () |
boost::shared_ptr< const AbstractOdeSystemInformation > | GetSystemInformation () const |
std::string | GetSystemName () const |
unsigned | GetNumberOfAttributes () const |
bool | HasAttribute (const std::string &rName) const |
double | GetAttribute (const std::string &rName) const |
unsigned | GetNumberOfStateVariables () const |
const std::vector< std::string > & | rGetStateVariableNames () const |
const std::vector< std::string > & | rGetStateVariableUnits () const |
unsigned | GetStateVariableIndex (const std::string &rName) const |
bool | HasStateVariable (const std::string &rName) const |
std::string | GetStateVariableUnits (unsigned index) const |
unsigned | GetNumberOfParameters () const |
const std::vector< std::string > & | rGetParameterNames () const |
const std::vector< std::string > & | rGetParameterUnits () const |
unsigned | GetParameterIndex (const std::string &rName) const |
bool | HasParameter (const std::string &rName) const |
std::string | GetParameterUnits (unsigned index) const |
unsigned | GetNumberOfDerivedQuantities () const |
const std::vector< std::string > & | rGetDerivedQuantityNames () const |
const std::vector< std::string > & | rGetDerivedQuantityUnits () const |
unsigned | GetDerivedQuantityIndex (const std::string &rName) const |
bool | HasDerivedQuantity (const std::string &rName) const |
std::string | GetDerivedQuantityUnits (unsigned index) const |
unsigned | GetAnyVariableIndex (const std::string &rName) const |
bool | HasAnyVariable (const std::string &rName) const |
std::string | GetAnyVariableUnits (unsigned index) const |
std::string | GetAnyVariableUnits (const std::string &rName) const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
Protected Member Functions inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::string | DumpState (const std::string &rMessage) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y) |
std::string | DumpState (const std::string &rMessage, std::vector< double > Y, double time) |
void | CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames) |
Protected Attributes inherited from AbstractOdeSystem | |
bool | mUseAnalyticJacobian |
Protected Attributes inherited from AbstractParameterisedSystem< std::vector< double > > | |
std::vector< double > | mStateVariables |
std::vector< double > | mParameters |
Protected Attributes inherited from AbstractUntemplatedParameterisedSystem | |
unsigned | mNumberOfStateVariables |
boost::shared_ptr< AbstractOdeSystemInformation > | mpSystemInfo |
Represents the Tyson & Novak (2001) system of ODEs. [doi:10.1006/jtbi.2001.2293]
Definition at line 51 of file TysonNovak2001OdeSystem.hpp.
TysonNovak2001OdeSystem::TysonNovak2001OdeSystem | ( | std::vector< double > | stateVariables = std::vector<double>() | ) |
Constructor.
stateVariables | optional initial conditions for state variables (only used in archiving) |
Definition at line 40 of file TysonNovak2001OdeSystem.cpp.
References Init(), OdeSystemInformation< ODE_SYSTEM >::Instance(), AbstractUntemplatedParameterisedSystem::mpSystemInfo, and AbstractParameterisedSystem< std::vector< double > >::SetStateVariables().
TysonNovak2001OdeSystem::~TysonNovak2001OdeSystem | ( | ) |
Destructor.
Definition at line 53 of file TysonNovak2001OdeSystem.cpp.
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virtual |
Compute the Jacobian of the ODE system.
rSolutionGuess | initial guess for the solution vector. |
jacobian | the Jacobian of the ODE system. |
time | at which to calculate the Jacobian. |
timeStep | used to calculate the Jacobian. |
Implements AbstractOdeSystemWithAnalyticJacobian.
Definition at line 161 of file TysonNovak2001OdeSystem.cpp.
References mJ3, mJ4, mJ5, mJ7, mJ8, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.
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Calculate whether the conditions for the cell cycle to finish have been met. (Used by CVODE solver to find exact stopping position)
time | at which to calculate whether the stopping event has occurred |
rY | value of the solution vector used to evaluate the RHS. |
Reimplemented from AbstractOdeSystem.
Definition at line 234 of file TysonNovak2001OdeSystem.cpp.
References EvaluateYDerivatives(), and mCycB_threshold.
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Calculate whether the conditions for the cell cycle to finish have been met. (Used by Chaste solvers to find whether or not to stop solving)
time | at which to calculate whether the stopping event has occurred |
rY | value of the solution vector used to evaluate the RHS. |
Reimplemented from AbstractOdeSystem.
Definition at line 224 of file TysonNovak2001OdeSystem.cpp.
References EvaluateYDerivatives(), and mCycB_threshold.
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Compute the RHS of the Alarcon et al. (2004) system of ODEs.
Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn']. An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].
time | used to evaluate the RHS. |
rY | value of the solution vector used to evaluate the RHS. |
rDY | filled in with the resulting derivatives (using Alarcons et al. (2004) system of equations). |
1. [CycB] 2. [Cdh1] 3. [Cdc20T] 4. [Cdc20A] 5. [IEP] 6. m - mass of the cell
Implements AbstractOdeSystem.
Definition at line 101 of file TysonNovak2001OdeSystem.cpp.
References mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK2d, mK2dd, mK3d, mK3dd, mK4, mK5d, mK5dd, mK6, mK7, mK8, mK9, mMad, mMstar, mMu, and mN.
Referenced by CalculateRootFunction(), and CalculateStoppingEvent().
void TysonNovak2001OdeSystem::Init | ( | ) |
Initialise parameter values.
Definition at line 58 of file TysonNovak2001OdeSystem.cpp.
References mCycB_threshold, mJ15, mJ16, mJ3, mJ4, mJ5, mJ7, mJ8, mK1, mK10, mK11, mK12d, mK12dd, mK12ddd, mK13, mK14, mK15d, mK15dd, mK16d, mK16dd, mK2d, mK2dd, mK2ddd, mK3d, mK3dd, mK4, mK4d, mK5d, mK5dd, mK6, mK7, mK8, mK9, mKeq, mMad, mMstar, mMu, and mN.
Referenced by TysonNovak2001OdeSystem().
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Serialize the object and its member variables.
archive | the archive |
version | the current version of this class |
Definition at line 144 of file TysonNovak2001OdeSystem.hpp.
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Definition at line 136 of file TysonNovak2001OdeSystem.hpp.
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Dimensionless parameter [CycB]_threshold.
Definition at line 68 of file TysonNovak2001OdeSystem.hpp.
Referenced by CalculateRootFunction(), CalculateStoppingEvent(), and Init().
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Dimensionless parameter J_15.
Definition at line 128 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensionless parameter J_16.
Definition at line 130 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensionless parameter J_3.
Definition at line 78 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter J_4.
Definition at line 80 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter J_5.
Definition at line 88 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter J_7.
Definition at line 96 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter J_8.
Definition at line 98 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Parameters for the Tyson & Novak (2001) model. Dimensional parameter k_1.
Definition at line 60 of file TysonNovak2001OdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensional parameter k_10.
Definition at line 104 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_11.
Definition at line 106 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_12'.
Definition at line 108 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_12''.
Definition at line 110 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_12'''.
Definition at line 112 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_13.
Definition at line 116 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_14.
Definition at line 118 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_15'.
Definition at line 120 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_15''.
Definition at line 122 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_16'.
Definition at line 124 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_16''.
Definition at line 126 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_2'.
Definition at line 62 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_2''.
Definition at line 64 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_2'''.
Definition at line 66 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_3'.
Definition at line 70 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_3''.
Definition at line 72 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_4.
Definition at line 76 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_4'.
Definition at line 74 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensional parameter k_5'.
Definition at line 82 of file TysonNovak2001OdeSystem.hpp.
Referenced by EvaluateYDerivatives(), and Init().
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Dimensional parameter k_5''.
Definition at line 84 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_6.
Definition at line 86 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_7.
Definition at line 92 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_8.
Definition at line 94 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter k_9.
Definition at line 102 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter K_eq.
Definition at line 114 of file TysonNovak2001OdeSystem.hpp.
Referenced by Init().
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Dimensionless parameter [Mad].
Definition at line 100 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter m_star.
Definition at line 134 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensional parameter mu.
Definition at line 132 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().
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Dimensionless parameter n.
Definition at line 90 of file TysonNovak2001OdeSystem.hpp.
Referenced by AnalyticJacobian(), EvaluateYDerivatives(), and Init().